Our long-term objective is to fully understand the molecular basis underlying tissue tropisms (throat versus skin) in group A streptococci (GAS; Streptococcus pyogenes), a bacterial pathogen causing high levels of disease in humans throughout the world. A first step towards this long-term goal is to characterize all genetic variation within the GAS population that differentiates organisms having strong preferences for the throat versus skin (specialists), or no clear cut preference (generalists). A next step is to determine which genotypes contribute to tissue-specific infection, by testing mutants in an experimental model that closely mimics disease. Final proof lies in the successful genetic conversion an organism of one tissue-specific phenotype to the other phenotype. Preliminary data suggest that tissue tropism in GAS is a complex genetic trait, involving multiple loci. The question raised on the molecular basis for tissue-specific GAS infections at the throat and skin is, in essence, the same as a fundamental question in ecology and evolutionary biology: What is the molecular basis for niche specialization, and how does it emerge? The proposed research (Aim 1) will provide a comprehensive assessment of the genetic variation within the GAS population that likely arises via recombination events (indels, orthologous gene displacements). Assuming that additional genotype candidates are uncovered, beyond those described in preliminary studies, the genotypes that are most likely to have a critical role in tissue tropism will be identified and the likely order of their acquisition will be delineated (Aim 2). New top-ranking genotype candidates for skin-specific infection will be inactivated in a skin specialist strain, and tested for altered growth at the skin using an in vivo model (Aim 3). If no new genotype candidates are uncovered (Aim 2), a throat strain specialist will be converted to a skin strain specialist (Aim 3). The proposed study will employ an integrated approach that combines tools of microbial genomics, epidemiology, evolutionary biology, and experimental pathogenesis. The findings will promote development of vaccines or therapies that break the chain of transmission, provide insights on the molecular changes surrounding the emergence of new virulent clones, and begin to address a fundamental question in evolutionary biology.